Figure 6.

Screen shot of a sequence read obtained with MAGIC-SPP. The sequence read was obtained from a publicly accessible implementation of MAGIC DB and is displayed with the MAGIC SeqView GUI available at that web site [22]. The upper window displays base calls; the lower provides phred quality scores in a histogram, with the first base call at the left. The quality-trimmed region provided by default parameters is in orange. The center of the gap at nucleotide 588 is highlighted in blue in the upper window and marked by a vertical blue line in the lower window. In a window of 10, the average error probability of this gap is 0.402, sufficient for Lucy to divide the high-quality region into two segments when used with default parameters [2]. Lucy would then pick the longest segment as its final output. In contrast, the length of the right-hand high quality segment is sufficient for the Gap-Join/Seq-Merge algorithm when used with default parameters to merge the two regions, providing an additional 102 high quality base calls in the final quality-trimmed output.